JJB, to be honest, what surprises me is why people don't use the most straight-forward way documented very explicitly in the installer which is simply
export PATH=/usr/local/clang7/bin:$PATH I never touch Makevars as that is very error-prone and makes it impossible to use multiple R versions. CRAN is already configured correctly for those compilers so you should not need to do any manual overrides. Cheers, Simon > On Dec 16, 2019, at 1:37 PM, Balamuta, James Joseph <balam...@illinois.edu> > wrote: > > Kasper, > > With all due respect, setting up the ~/.R/Makevars file is a key step that > trips up a majority of users. Sadly, the documentation for Makevars is not > beginner friendly and is scattered across multiple manuals [1][2] with the > most precise explanation being off-site [3]. Moreover, many do not know about > R's startup files [4], how to modify them, or where they exist as dot files > are hidden by default [5]. > > I've toyed with many solutions over the years, including but not limited to: > providing an R script to write the lines to ~/.R/Makevars, emphasizing that > `file.edit()` can be used to open the configuration files, providing > step-by-step guides, and so on. The most successful approach taken was to > provide as much of an automated process as possible while emphasizing the > steps for those who wanted more depth. > > Having said this, my dream is for the macOS CRAN binary to come with > everything configured and setup correctly. Until that is the case or there > exists a better approach, I'm more inclined to stick with the current > approach I've taken especially as the macOS toolchain's stability changes on > minor point releases (MAJOR.MINOR.PATCH). Again, these are made freely > available to address an ever clearer need that is arising in the community. > > Best, > > JJB > > [1]: R Installation and Administration, Section 6.3.2: macOS, > https://cran.r-project.org/doc/manuals/R-admin.html#macOS-packages > [2]: Writing R Extensions, Section 1.2.1: Using Makevars, > https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-Makevars > [3]: StackOverflow, Understanding the contents of the Makevars file in R > (macros, variables, ~/.R/Makevars and pkg/src/Makevars), > https://stackoverflow.com/q/43597632/1345455 > [4]: Initialization at Start of an R Session > https://stat.ethz.ch/R-manual/R-patched/library/base/html/Startup.html > [5]: How to Show Hidden Files on a Mac > https://www.macrumors.com/how-to/show-hidden-files-on-a-mac/ > > On 12/16/19, 9:39 AM, "R-SIG-Mac on behalf of Kasper Daniel Hansen" > <r-sig-mac-boun...@r-project.org on behalf of kasperdanielhan...@gmail.com> > wrote: > > Just a comment on the macos-rtools. It seems wrong to me to set the user > level ~/.R/Makevars. > > On Sat, Dec 14, 2019 at 9:29 PM Manuel Spínola <mspinol...@gmail.com> > wrote: > >> Thank you very much John. >> >> I restarted my computer, and everything looks fine now, I fitted a brms >> model without the error message. >> >> Manuel >> >> El sáb., 14 dic. 2019 a las 19:45, Fox, John (<j...@mcmaster.ca>) >> escribió: >> >>> Dear Manuel, >>> >>> As far as I can tell, a lot of people are experiencing problems with >> rstan >>> under Catalina -- I don't use brms but rather rstan directly, and I >>> thrashed around quite a bit to get it work reliably (at least so far!). >>> >>> The final bit of the puzzle for me was to modify Makevars in the .R >>> subdirectory of my home directory according to the instructions at < >>> https://discourse.mc-stan.org/t/dealing-with-catalina-ii/11802/74>. >> Maybe >>> that will work for you too. If this is in fact a generally satisfactory >>> solution, one would hope that it could be made more convenient for macOS >>> rstan users. >>> >>> I hope this helps, >>> John >>> >>> ----------------------------- >>> John Fox, Professor Emeritus >>> McMaster University >>> Hamilton, Ontario, Canada >>> Web: http::/socserv.mcmaster.ca/jfox >>> >>>> On Dec 14, 2019, at 6:28 PM, Manuel Spínola <mspinol...@gmail.com> >>> wrote: >>>> >>>> Dear list members, >>>> >>>> I updated everything, Catalina, Xcode, CLT, R 3.6.2, rstan from source, >>> and >>>> installed the r-macos-rtools, but I still have problems. >>>> >>>> library(brms) >>>> group <- rep(c("treat", "placebo"), each = 30) >>>> symptom_post <- c(rnorm(30, mean = 1, sd = 2), rnorm(30, mean = 0, sd = >>> 1)) >>>> dat1 <- data.frame(group, symptom_post) >>>> >>>> fit1 <- brm(bf(symptom_post ~ group, sigma ~ group), >>>> data = dat1, family = gaussian()) >>>> >>>> Chain 4: Iteration: 1 / 2000 [ 0%] (Warmup) >>>> [1] "Error in sampler$call_sampler(args_list[[i]]) : " >>>> [2] " c++ exception (unknown reason)" >>>> error occurred during calling the sampler; sampling not done >>>> >>>> >>>> >>>> >>>> >>>> >>>> El jue., 12 dic. 2019 a las 12:51, Balamuta, James Joseph (< >>>> balam...@illinois.edu>) escribió: >>>> >>>>> Greetings and Salutations All, >>>>> >>>>> Great to see the `r-macos-rtools` installer popping up! As the author >> of >>>>> it, please note that it's an unofficial (non-CRAN backed) installer >> that >>>>> seeks to automatically establish the CRAN toolchain in a friendly GUI >>>>> installer. We developed it to help out students in STAT 385 @ UIUC [ >>>>> http://stat385.com/ ] setup the correct developer environment in a >>>>> uniform manner as there wasn't really any prior installer packages >> made >>>>> available at the time. We're grateful for the financial support that >> was >>>>> given by Timothy Bates to sign the installer. >>>>> >>>>> With this being said, each step the installer takes is documented >>> across a >>>>> README file, installer splash screen, and by a post. >>>>> >>>>> README Overview: >>>>> >> https://github.com/rmacoslib/r-macos-rtools#what-does-the-installer-do >>>>> Installer Splash: >>>>> >>> >> https://raw.githubusercontent.com/rmacoslib/r-macos-rtools/master/readme_img/lock_icon.png >>>>> Post: >>>>> >>> >> https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/ >>>>> >>>>> That said, there is also Appendix C.3 macOS of R Installation and >>>>> Administration [ >>>>> https://cran.r-project.org/doc/manuals/r-release/R-admin.html#macOS ] >>>>> that goes over the details in greater depth. >>>>> >>>>> For those who are worried about security, please note that we've taken >>>>> steps to ensure secure downloads by verifying the installer hashes >>> prior to >>>>> installing per prior remarks by Simon regarding earlier versions of >> the >>>>> installer [ see the prior discussion and my response here: >>>>> https://stat.ethz.ch/pipermail/r-sig-mac/2018-May/012745.html ]. >>>>> >>>>> Lastly, and perhaps more critically, please note that just using Xcode >>> CLI >>>>> is not sufficient as it does not match the prescribed compilation >>> toolchain >>>>> (clang7 with OpenMP enabled and gfortran). >>>>> >>>>> Best, >>>>> >>>>> JJB >>>>> >>>>> On 12/11/19, 7:25 PM, "R-SIG-Mac on behalf of Manuel Spínola" < >>>>> r-sig-mac-boun...@r-project.org on behalf of mspinol...@gmail.com> >>> wrote: >>>>> >>>>> An update. >>>>> >>>>> Before doing the suggested installation, I updated Catalina to >>> 10.5.2, >>>>> Xtools to 11.3 and the Command Line Tools and it works. >>>>> >>>>> Manuel >>>>> >>>>> El mié., 11 dic. 2019 a las 16:05, Ken Beath (<k...@kjbeath.com.au >>> ) >>>>> escribió: >>>>> >>>>>> No, it only downloads and installs the right compilers and updates >>>>>> Makevars and REnvirons. These are what Stan and RCpp require so you >>>>> could >>>>>> do these manually. >>>>>> >>>>>> What it does is described at >>>>> https://github.com/rmacoslib/r-macos-rtools >>>>>> >>>>>> Ken >>>>>> >>>>>>> On 12 Dec 2019, at 1:14 am, Manuel Spínola <mspinol...@gmail.com> >>>>> wrote: >>>>>>> >>>>>>> Thank you very much to all. >>>>>>> >>>>>>> Does Installing the macos-rtools could affect R in other ways? >>>>>>> >>>>>>> Manuel >>>>>>> >>>>>>> El mié., 11 dic. 2019 a las 6:56, Ken Beath (<k...@kjbeath.com.au>) >>>>>> escribió: >>>>>>> What worked for me was installing the tools using >>>>>> https://github.com/rmacoslib/r-macos-rtools/releases >>>>>>> >>>>>>> and then installing rstan from source ie >>>>>> install.packages(“rstan”,type=“source) as suggested on one of the >>>>> stan >>>>>> forums >>>>>>> >>>>>>> Ken >>>>>>> >>>>>>>> On 11 Dec 2019, at 11:09 am, Manuel Spínola < >>>>> mspinol...@gmail.com> >>>>>> wrote: >>>>>>>> >>>>>>>> Dear list members, >>>>>>>> >>>>>>>> When trying to fit this example from the CRAN repository fro >>>>> brms, I >>>>>> got >>>>>>>> the following error message after the 4th chain. I am using R >>>>> 3.6.1 in >>>>>>>> Catalina MacOS. >>>>>>>> >>>>>>>> >>>>>>>> library(brms) >>>>>>>> >>>>>>>> group <- rep(c("treat", "placebo"), each = 30) >>>>>>>> symptom_post <- c(rnorm(30, mean = 1, sd = 2), rnorm(30, mean = >>>>> 0, sd >>>>>> = 1)) >>>>>>>> dat1 <- data.frame(group, symptom_post) >>>>>>>> >>>>>>>> fit1 <- brm(bf(symptom_post ~ group, sigma ~ group), >>>>>>>> data = dat1, family = gaussian()) >>>>>>>> >>>>>>>> >>>>>>>> [1] "Error in sampler$call_sampler(args_list[[i]]) : " >>>>>>>> [2] " c++ exception (unknown reason)" >>>>>>>> error occurred during calling the sampler; sampling not done >>>>>>>> >>>>>>>> I think is a problem with Catalina MacOS, but I don´t know how to >>>>>> solve it. >>>>>>>> >>>>>>>> Manuel >>>>>>>> >>>>>>>> -- >>>>>>>> *Manuel Spínola, Ph.D.* >>>>>>>> Instituto Internacional en Conservación y Manejo de Vida >>>>> Silvestre >>>>>>>> Universidad Nacional >>>>>>>> Apartado 1350-3000 >>>>>>>> Heredia >>>>>>>> COSTA RICA >>>>>>>> mspin...@una.cr <mspin...@una.ac.cr> >>>>>>>> mspinol...@gmail.com >>>>>>>> Teléfono: (506) 8706 - 4662 >>>>>>>> Personal website: Lobito de río < >>>>>> https://sites.google.com/site/lobitoderio/> >>>>>>>> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/> >>>>>>>> >>>>>>>> [[alternative HTML version deleted]] >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> R-SIG-Mac mailing list >>>>>>>> R-SIG-Mac@r-project.org >>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Manuel Spínola, Ph.D. >>>>>>> Instituto Internacional en Conservación y Manejo de Vida Silvestre >>>>>>> Universidad Nacional >>>>>>> Apartado 1350-3000 >>>>>>> Heredia >>>>>>> COSTA RICA >>>>>>> mspin...@una.cr >>>>>>> mspinol...@gmail.com >>>>>>> Teléfono: (506) 8706 - 4662 >>>>>>> Personal website: Lobito de río >>>>>>> Institutional website: ICOMVIS >>>>>> >>>>>> >>>>> >>>>> -- >>>>> *Manuel Spínola, Ph.D.* >>>>> Instituto Internacional en Conservación y Manejo de Vida Silvestre >>>>> Universidad Nacional >>>>> Apartado 1350-3000 >>>>> Heredia >>>>> COSTA RICA >>>>> mspin...@una.cr <mspin...@una.ac.cr> >>>>> mspinol...@gmail.com >>>>> Teléfono: (506) 8706 - 4662 >>>>> Personal website: Lobito de río < >>>>> https://sites.google.com/site/lobitoderio/> >>>>> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/> >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> R-SIG-Mac mailing list >>>>> R-SIG-Mac@r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>>> >>>>> >>>>> >>>> >>>> -- >>>> *Manuel Spínola, Ph.D.* >>>> Instituto Internacional en Conservación y Manejo de Vida Silvestre >>>> Universidad Nacional >>>> Apartado 1350-3000 >>>> Heredia >>>> COSTA RICA >>>> mspin...@una.cr <mspin...@una.ac.cr> >>>> mspinol...@gmail.com >>>> Teléfono: (506) 8706 - 4662 >>>> Personal website: Lobito de río < >>> https://sites.google.com/site/lobitoderio/> >>>> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> R-SIG-Mac mailing list >>>> R-SIG-Mac@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >>> >> >> -- >> *Manuel Spínola, Ph.D.* >> Instituto Internacional en Conservación y Manejo de Vida Silvestre >> Universidad Nacional >> Apartado 1350-3000 >> Heredia >> COSTA RICA >> mspin...@una.cr <mspin...@una.ac.cr> >> mspinol...@gmail.com >> Teléfono: (506) 8706 - 4662 >> Personal website: Lobito de río < >> https://sites.google.com/site/lobitoderio/> >> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > > > -- > Best, > Kasper > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
